Variant report

Variant	rs7628889
Chromosome Location	chr3:150305914-150305915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150305838-150306071	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:150305702-150306917	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:150305845-150306101	K562	blood:	n/a	n/a
4	POLR2A	chr3:150305731-150306307	U87	brain:	n/a	n/a
5	POLR2A	chr3:150305854-150306416	A549	lung:	n/a	n/a
6	POLR2A	chr3:150305844-150306216	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:150305725-150306436	U87	brain:	n/a	n/a
8	POLR2A	chr3:150304166-150307088	K562	blood:	n/a	n/a
9	POLR2A	chr3:150305821-150306841	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150264606..150266340-chr3:150304778..150306324,2	MCF-7	breast:
2	chr3:150304290..150306605-chr3:150321050..150322938,2	K562	blood:
3	chr3:150295926..150298011-chr3:150304810..150307775,2	MCF-7	breast:

No data

Variant related genes	Relation type
SERP1	TF binding region
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1133494	1.00[ASN][1000 genomes]
rs12695957	0.82[AFR][1000 genomes]
rs14434	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818788	0.89[ASN][1000 genomes]
rs1915942	0.89[ASN][1000 genomes]
rs1915943	0.89[ASN][1000 genomes]
rs2049229	1.00[ASN][1000 genomes]
rs2090916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868946	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868947	1.00[ASN][1000 genomes]
rs6440683	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440684	0.84[ASN][1000 genomes]
rs6440685	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6764672	0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6790726	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7374917	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7631671	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638500	1.00[ASN][1000 genomes]
rs7642917	1.00[ASN][1000 genomes]
rs8052	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9289818	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9289820	0.84[ASN][1000 genomes]
rs9289821	0.89[ASN][1000 genomes]
rs954068	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9809820	0.87[ASN][1000 genomes]
rs9819287	0.89[ASN][1000 genomes]
rs9820529	0.81[ASN][1000 genomes]
rs9836797	0.85[ASN][1000 genomes]
rs9865177	0.89[ASN][1000 genomes]
rs9871517	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7628889	EIF2A	cis	Artery Tibial	GTEx
rs7628889	EIF2A	cis	lung	GTEx
rs7628889	EIF2A	cis	hippocampus	BrainEAC
rs7628889	EIF2A	cis	putamen	BrainEAC
rs7628889	EIF2A	cis	frontal cortex	BrainEAC
rs7628889	EIF2A	cis	cerebellar cortex	BrainEAC
rs7628889	EIF2A	cis	temporal cortex	BrainEAC
rs7628889	EIF2A	cis	substantia nigra	BrainEAC
rs7628889	EIF2A	cis	intralobular white matter	BrainEAC
rs7628889	EIF2A	cis	inferior olivary nucleus	BrainEAC
rs7628889	EIF2A	cis	brain	BrainEAC
rs7628889	EIF2A	cis	Thyroid	GTEx
rs7628889	EIF2A	cis	Nerve Tibial	GTEx
rs7628889	EIF2A	cis	Esophagus Muscularis	GTEx
rs7628889	EIF2A	cis	thalamus	BrainEAC
rs7628889	EIF2A	cis	occipital cortex	BrainEAC

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:150266000-150307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:150278000-150306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:150278400-150306400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:150280200-150307800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:150291600-150306200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:150294200-150314600	Weak transcription	Psoas Muscle	Psoas
9	chr3:150294400-150306600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:150295200-150306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:150295400-150307200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:150295600-150318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:150297400-150306400	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:150298000-150306400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150300800-150316200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:150301600-150306600	Strong transcription	GM12878-XiMat	blood
17	chr3:150301600-150320200	Weak transcription	Small Intestine	intestine
18	chr3:150302400-150320000	Weak transcription	Brain Germinal Matrix	brain
19	chr3:150302600-150307600	Weak transcription	NHDF-Ad	bronchial
20	chr3:150303000-150306000	Weak transcription	Primary B cells from cord blood	blood
21	chr3:150303000-150316400	Weak transcription	HUVEC	blood vessel
22	chr3:150303200-150306000	Weak transcription	Right Ventricle	heart
23	chr3:150303200-150307000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:150303400-150316800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:150303600-150306000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:150303600-150306200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:150303600-150306400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:150303600-150306400	Weak transcription	Gastric	stomach
29	chr3:150303600-150307400	Weak transcription	Stomach Mucosa	stomach
30	chr3:150303600-150308000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:150303600-150308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:150303600-150310400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:150303600-150315600	Weak transcription	HMEC	breast
34	chr3:150303600-150317400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:150303600-150319200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:150303800-150306000	Weak transcription	Placenta	Placenta
37	chr3:150303800-150306000	Weak transcription	HSMMtube	muscle
38	chr3:150303800-150306200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:150303800-150307000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:150303800-150307600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:150303800-150307800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:150303800-150307800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:150303800-150307800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:150303800-150308000	Weak transcription	Aorta	Aorta
45	chr3:150303800-150308600	Weak transcription	Adipose Nuclei	Adipose
46	chr3:150303800-150308800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:150303800-150309400	Weak transcription	Esophagus	oesophagus
48	chr3:150303800-150310000	Weak transcription	Osteobl	bone
49	chr3:150303800-150310600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:150303800-150313800	Weak transcription	Pancreas	Pancrea

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